1. DNA Replication 17 September 2013

2. Note: On all figures: Template strand (parental DNA) in orange Primer strand (newly synthesized DNA) in red.

3. DNA Synthesis Reaction

4. Adding one nucleotide High energy bond is cleaved Pyrophosphate is hydrolyzed into 2 inorganic phosphates

5. Replication is semi-conservative

6. Replication Fork (incorrect mechanism)

7. Replication Fork

8. Editing by DNA Polymerase

10. Editing Sites in DNA Polymerase

11. Proofreading: another reason why 3’ to 5’ synthesis is not possible Note: To make a phosphodiester bond, you need 3 phosphates, two of which are eliminated.

12. Site-directed mismatch repair

13. Video Suggestions http://www.youtube.com/watch?v=dgPh1qigv7s http://www.youtube.com/watch?v=HYS6EKnQcv0

15. Replication machinery

16. Making primers

17. Okazaki Fragment Synthesis Prokaryotes: DNA Polymerase I removes RNA primers. Eukaryotes: FLAP endonuclease (FEN-1) removes RNA primers.

18. –DNA Polymerase I : Fills the gaps during DNA repair. –DNA Polymerase II : repairs a fork that is stalled because of DNA damage –DNA Polymerase III : Is responsible for DNA replication. The three main DNA Polymerases in E. coli.

19. DNA Helicase

20. SSB Proteins

21. Sliding Clamp

22. Okazaki Fragment Synthesis

23. Replication machinery in prokaryotes

24. Video suggestion http://www.youtube.com/watch?v=-mtLXpgjHL0&feature=related

25. Replication machinery in prokaryotes

26. Replication machinery in eukaryotes ε

27. Unwinding of the double helix and replication Replication speed (bacteria): 500 nucleotides per second. Need to unwind 50 turns of the double helix per second.

28. Topoisomerase I: mechanism of action

29. Histones and Replication

31. Histone modifications are copied during replication.